Nature 2020 01 30 Part.02

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nature research | life sciences reporting summary

November 2017

6. Statistical parameters
   For all figures and tables that use statistical methods, confirm that the following items are present in relevant figure legends (or in the
   Methods section if additional space is needed).

n/a Confirmed

The exact sample size (n) for each experimental group/condition, given as a discrete number and unit of measurement (animals, litters, cultures, etc.)

A description of how samples were collected, noting whether measurements were taken from distinct samples or whether the same

sample was measured repeatedly

A statement indicating how many times each experiment was replicated

The statistical test(s) used and whether they are one- or two-sided

Only common tests should be described solely by name; describe more complex techniques in the Methods section.

A description of any assumptions or corrections, such as an adjustment for multiple comparisons

Test values indicating whether an effect is present

Provide confidence intervals or give results of significance tests (e.g. P values) as exact values whenever appropriate and with effect sizes noted.

A clear description of statistics including central tendency (e.g. median, mean) and variation (e.g. standard deviation, interquartile range)

Clearly defined error bars in all relevant figure captions (with explicit mention of central tendency and variation)

See the web collection on statistics for biologists for further resources and guidance.

` Software

Policy information about availability of computer code

7. Software
   Describe the software used to analyze the data in this
   study.

Analysis of mass spectra: MSGF+ software v10072

Sequence processing: Picard 2.9.4

Metagenome and metatranscriptome profiles generated using bioBakery meta’omics

workflow v0.9.0 (Preprocessing: KneadData 0.7.0; Taxonomic profiles: MetaPhlAn2 v2.6.0;

Functional profiles: HUMAnN2 v0.11.0 with UniRef release 2014_07, Diamond v0.8.22.84)

Viral profiles: VirMAP

16S analysis: USEARCH v7.0.1090

Data analysis and plotting: R (main packages: edgeR, nlme, ggplot2, ggridges, pheatmap,

vegan, tsne), Julia plots package

Network construction and visualization: HAllA 0.8.17, Cytoscape 3.6.0

For manuscripts utilizing custom algorithms or software that are central to the paper but not yet described in the published literature, software must be made

available to editors and reviewers upon request. We strongly encourage code deposition in a community repository (e.g. GitHub). Nature Methods guidance for

providing algorithms and software for publication provides further information on this topic.

` Materials and reagents

Policy information about availability of materials

8. Materials availability
   Indicate whether there are restrictions on availability of
   unique materials or if these materials are only available
   for distribution by a third party.

Remaining biospecimen aliquots from the project are available by request from the

corresponding author.

9. Antibodies
   Describe the antibodies used and how they were validated
   for use in the system under study (i.e. assay and species).

Antibodies were used for serology and the ELISAs we performed are not commercially

available as kits or reagents (except for secondary antibodies).

The primary antibodies are patient sera (validation not applicable).

Conjugated polyclonal secondary antibodies are utilized, clone not applicable:

Jackson ImmunoResearch Laboratories goat anti-human IgG-alkaline phosphatase; Cat #

109-056-098; 1:1000 dilution

Jackson ImmunoResearch Laboratories goat anti-human IgA-alkaline phosphatase; Cat #

109-055-011; 1:1000 dilution